Tag: footprint based TF activity
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How to Analyze Single-Cell RNA-seq Data — Complete Beginner’s Guide Part 16: Build Gene Regulatory Networks with decoupleR and CollecTRI
Infer per-cell transcription factor activity from a curated, signed regulatory network — no de novo network learning, no motif databases, just one fast linear model. In Part 15 you learned to redraw the entire scRNA-seq series with cleaner code. Now we return to biology with a new question: which transcription factors are driving each cell…
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Recent Posts
- How to Analyze Single-Cell RNA-seq Data — Complete Beginner’s Guide Part 16: Build Gene Regulatory Networks with decoupleR and CollecTRI
- How to Analyze Single-Cell RNA-seq Data — Complete Beginner’s Guide Part 15: Better Visualization with scplotter
- How to Analyze Single-Cell RNA-seq Data — Complete Beginner’s Guide Part 14: Cell Fate Probability Analysis with CellRank
- How to Analyze Single-Cell RNA-seq Data — Complete Beginner’s Guide Part 13: RNA Velocity Analysis with scVelo
Tags
Alternative Splicing Analysis ATAC-seq BAM ChIP-seq chromatin accessibility CNV DESeq2 Differential Expression edgeR FASTQ GATK Mutect2 gene expression heatmap HOMER HPC Isoform limma MACS2 MAF miRNA miRNA-seq MSigDB Normalization peak calling RNA-seq SLURM somatic mutations Transcript VCF whole genome sequencing